Align 2-deoxy-D-ribonate transporter (characterized)
to candidate WP_012385061.1 BIND_RS10525 MFS transporter
Query= reanno::Burk376:H281DRAFT_00642 (448 letters) >NCBI__GCF_000019845.1:WP_012385061.1 Length = 437 Score = 278 bits (710), Expect = 3e-79 Identities = 158/417 (37%), Positives = 228/417 (54%), Gaps = 10/417 (2%) Query: 17 ATRKAMARLIPLMCAIYFMSFLDRTNVALAKLQLAADVGISAAAYGFGSGIFFLGYALLE 76 A RK R++P + Y +++LDR NV AKLQ+A D+ S A YG G+GIFFLGY L E Sbjct: 22 AYRKVFWRIVPFLMVCYVVAYLDRINVGFAKLQMAQDLQFSEAVYGLGAGIFFLGYFLFE 81 Query: 77 VPSNLAAHKVGPRRWIARIAVTWGILSTAMMFVQGTSSFYVLRVLLGIAEAGLFPALMYM 136 +PSNL HKVG R WIARI VTWG++S A +FV +FYV+R LLG+AEAG +P ++ Sbjct: 82 IPSNLILHKVGARVWIARIMVTWGLISAAFIFVGSAPAFYVMRFLLGMAEAGFYPGIILY 141 Query: 137 VTLWFAPHDRPVVVGWIYIAPALALMLGNPLGGALM-QLDGFGGLHGWQWMFMLEGIPSV 195 +T W+ + R ++ A ++ + GNPL G +M Q GGL GWQWMF++E +P+V Sbjct: 142 LTFWYPSYKRAKIIAIFMAAIPVSGIFGNPLSGWIMDQFHHTGGLAGWQWMFLIEAVPAV 201 Query: 196 IVGIVLFFKMPERPRDARWLSAAERDVLETHAVIDGHGRADYSSANWIAALKRPTTVLIG 255 IVGI+ +F + RDA+WLS E+ +LE + R S + P + Sbjct: 202 IVGIITYFYLDNNIRDAKWLSDDEKQILEQNIKAQAAQRETTHSLRQV--FTNPRIWQMA 259 Query: 256 LIYFLNQVAFVGLYFFTPAIIHQMHVDSSLVVGFLSASVGLGFLLGVLVLPRIHRRTDRD 315 IYF GL F+ P + + V + +G +SA + FL V+V+ R D Sbjct: 260 FIYFAVVTGQYGLTFWMPTFVKTVGVTGNFNIGLISA---IPFLCAVVVMIAFGRSADHY 316 Query: 316 CVFLGILTAGLILGACAYLA---VTNPAARIALLTVTAFFAGGVLPSYWAIAMKRLQGIQ 372 L +LGA ++A TN I L++ A A P +W++ L G Sbjct: 317 RERRWHLAIPALLGAVGFIAAATTTNMGFAILFLSLAAAGALTCAPLFWSLPTAFLSGTA 376 Query: 373 AAAGLAFVNTIGLIGGFVGPYLFGIAETSSGRSDAGFTVILIAGVLGLALVPVLARA 429 AA G+A +N+IG + GFV PY+ G+ ++G + + VLG A+V +L A Sbjct: 377 AAGGIAMINSIGNLAGFVSPYVIGMIRDATGNTQYAMYTLAAMLVLG-AIVTLLTPA 432 Lambda K H 0.329 0.142 0.436 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 577 Number of extensions: 31 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 448 Length of database: 437 Length adjustment: 32 Effective length of query: 416 Effective length of database: 405 Effective search space: 168480 Effective search space used: 168480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory